Puriney
commented
4 years ago Sorry that I found this line in the README:
In --umi mode, the coverage table reports the number of unambiguous UMIs that support reference or alternate allele per cell.
In addition, by running the test example, I am sure the number of UMIs is counted in this case.
$ vartrix -v vartrix/test/test.vcf.gz \
-b vartrix/github/vartrix/test/test.bam \
-f vartrix/test/test.fa -c outcome2/vartrix_colnames.txt \
-o outcome2/vartrix_res.n_alt_reads.mtx \
--ref-matrix outcome2/vartrix_res.n_ref_reads.mtx \
--scoring-method coverage \
$ vartrix -v vartrix/test/test.vcf.gz \
-b vartrix/github/vartrix/test/test.bam \
-f vartrix/test/test.fa -c outcome2/vartrix_colnames.txt \
-o outcome2/vartrix_res.n_alt_reads_umi.mtx \
--ref-matrix outcome2/vartrix_res.n_ref_reads_umi.mtx \
--scoring-method coverage --umi\
$ diff outcome2//vartrix_res.n_alt_reads.mtx outcome2//vartrix_res.n_alt_reads_umi.mtx
7c7
< 3 18 7
---
> 3 18 1
'--scoring-method coverage' would count the number of alt / ref reads. But I was wondering if the number of alt / ref UMIs would be output when additionally '--umi' is called?